Error trickered on both CentOS and RHEL system.
It was found, that our schared cshr file for our linux computers,
setup a LD_LIBRARY_PATH which made the problems.
Here is backtrack how to solve the problems, and the solution.
-----------------------------
To trick the error.
python -c "from scipy.linalg import clapack"
Solution found, following this link:
https://bugzilla.redhat.com/show_bug.cgi?id=709782
The solution was finding out which atlas and lapach which was installed:
rpm -qa|grep atlas
rpm -qa|grep lapack
Inspecting if libclapack was at the local computer.
rpm -ql lapack | grep libclapack
rpm -ql atlas | grep libclapack
This showed the files where in:
/usr/lib64/atlas/libclapack.so.3
/usr/lib64/atlas/libclapack.so.3.0
That means, some PATH directions must be wrong.
echo $LD_LIBRARY_PATH
Which have hint to, that /usr/lib64 not part of the that path.
unsetenv LD_LIBRARY_PATH
python -c "from scipy.linalg import clapack"
Showed it now was working.
Unsetting LD_LIBRARY_PATH, and then run python, would
the automatically set the right LD_LIBRARY_PATH.
Problem was related to a shared "cshrc", which set the
LD_LIBRARY_PATH
to folder of files, which is needed by other programs, but interferes with
the local python scipy installation.
The solution, was to create a set of shell files, which unset
the LD_LIBRARY_PATH. In the same time, it makes sure and
ssh connection is established to the one dedicated linux computer
where software packages have been met for the installation.
--------- relax300
#!/bin/tcsh -f
# Set the lax version used for this script.
set RELAX=/sbinlab2/software/NMR-relax/relax-3.0.0/relax
# Remove env set to wrong library files.
unsetenv LD_LIBRARY_PATH
# Check machine, since only machine haddock have correct pakages installed
if ( $HOST != "haddock") then
echo "You have to run on haddock. I do it for you"
ssh haddock -Y -t "cd $PWD; unsetenv LD_LIBRARY_PATH; $RELAX $argv; /bin/tcsh"
else
$RELAX $argv
endif
--------- relax_trunk
#!/bin/tcsh -f
# Set the lax version used for this script.
set RELAX=/sbinlab2/software/NMR-relax/relax_trunk/relax
# Remove env set to wrong library files.
unsetenv LD_LIBRARY_PATH
# Check machine, since only machine haddock have correct pakages installed
if ( $HOST != "haddock") then
echo "You have to run on haddock. I do it for you"
ssh haddock -Y -t "cd $PWD; unsetenv LD_LIBRARY_PATH; $RELAX $argv; /bin/tcsh"
else
$RELAX $argv
endif
----------- relax_disp
#!/bin/tcsh -f
# Set the lax version used for this script.
set RELAX=/sbinlab2/software/NMR-relax/relax_disp/relax
# Remove env set to wrong library files.
unsetenv LD_LIBRARY_PATH
# Check machine, since only machine haddock have correct pakages installed
if ( $HOST != "haddock") then
echo "You have to run on haddock. I do it for you"
ssh haddock -Y -t "cd $PWD; unsetenv LD_LIBRARY_PATH; $RELAX $argv; /bin/tcsh"
else
$RELAX $argv
endif
Troels Emtekær Linnet
2013/8/18 Edward d Auvergne <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
Update of bug #21032 (project relax):
Status: None => Invalid
Open/Closed: Open => Closed
_______________________________________________________
Follow-up Comment #1:
This is a Scipy rather than relax bug. You can test this by running Python
and typing:
from scipy.linalg import expm
This will show that the currently installed Scipy is broken. I have to
close
the bug as it is not fixable from within relax.
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?21032>
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Re: [bug #21032] running relax disp branch, undefined symbol clapack-sgesv in scipy linalg.